Ann Killion, Chronicle columnist, is seen on Monday, Dec. 10, 2012 in San Francisco, Calif.

Ann Killion, Chronicle columnist, is seen on Monday, Dec. 10, 2012 in San Francisco, Calif.

Photo: Russell Yip, The Chronicle

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San Francisco 49ers' Colin Kaepernick passes in 1st quarter of 34-0 loss to Denver Broncos during NFL preseason game at Levi's Stadium in Santa Clara, Calif. on Sunday, August 17, 2014.

San Francisco 49ers' Colin Kaepernick passes in 1st quarter of 34-0 loss to Denver Broncos during NFL preseason game at Levi's Stadium in Santa Clara, Calif. on Sunday, August 17, 2014.

Photo: Scott Strazzante, The Chronicle

In Week 3 of preseason, pressure grows for 49ers

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It is Week 3 of the NFL preseason. The most important week. The time when the first teams are supposed to click, when the backup positions become clear, when the hard work done in training camp shows on the field.

Which means the 49ers have an awful lot to do before Sunday's practice game against San Diego.

"This is going to be an important week for us, a big week," head coach Jim Harbaugh said after the 49ers were manhandled by the Denver Broncos 34-0 on Sunday. "We need improvement. We need to make decisions on who we're playing with. We've got to tighten this down fast. ... It's off right now."

Harbaugh's remarks were telling. The coach who usually describes performances as "A-plus-plus," players as "trusted agents" and practice as "a life cycle" exhibited honest, legitimate concern about his team's readiness.

You can't put too much stock in preseason results, so the team's 0-2 record and position on the wrong end of a combined 57-3 score aren't huge concerns. But there are some performances with which one can justifiably be troubled, even in preseason.

For the second straight year, the 49ers don't appear to have a competent answer to carry a clipboard behind Colin Kaepernick. A year after Colt McCoy struggled in preseason and then couldn't be trusted to handle a single important snap in the regular season, the 49ers turned to Blaine Gabbert. And he has been awful in two preseason games.

Whatever the Harbaugh magic is with quarterbacks, it hasn't translated to backups. After having an obvious and capable quarterback hierarchy in his first two seasons as coach - Alex Smith backed up by heir apparent Kaepernick and then Kaepernick backed up by mentor Smith - Harbaugh is facing another season of question marks at the No. 2 position.

"In terms of a backup quarterback, it'll be as simple as whoever doesn't turn the ball over," Harbaugh said. "They're turning the ball over. All of them have. There's no one to elevate."

But Harbaugh dismissed any talk of trying to look for another quarterback at this stage of the game. So the job will go to Gabbert, Josh Johnson or McLeod Bethel-Thompson.

This is a serious issue, for a variety of reasons. Because of injuries, inexperience and a looming suspension for Aldon Smith (hey, any time you're ready to issue an edict, Emperor Goodell), the 49ers' defense may not be as impenetrable as it has been in past seasons. There's some thought that, especially early in the season without NaVorro Bowman and Smith, the 49ers will have to rely on their offense to win games, as opposed to leaving outcomes in the hands of a defense that has dominated in the Harbaugh era.

But to do that, the 49ers are going to have to open up the offense, and expand Kaepernick's bag of tricks. Kaepernick's best weapon remains his legs, but running makes him extremely vulnerable to injury.

Even if he isn't running with the ball, a wider-open offense will leave him more exposed. Kaepernick started all 19 games last season, but suffered a foot injury that limited him early in the season. Harbaugh relied on an offense that reduced Kaepernick's exposure but was often ineffective, especially in the red zone.

The reality is that Kaepernick is at his best when he's playing a high-risk style. That means a competent backup may be even more important for the 49ers than it is for many teams.

There are other concerns with the offense, which was, unfortunately, in midseason form in at least one area Sunday: with a wasted timeout during the first drive. And rather than try to establish rhythm with his receivers, Kaepernick threw deep passes to the end zone, which fell incomplete, to stall both of his drives. Most observers would say that what this team really needs to practice most is red zone efficiency, not 30-plus-yard throws into the end zone.

The 49ers signed a team-friendly deal with Kaepernick, which will ostensibly allow them to sign other players. They owe it to the offense to get Alex Boone back into the fold as quickly as possible. Gil Brandt reported on the NFL Network that Boone had turned down an offer that would make him one of the top-paid guards in the league. Other outlets cast doubt on Brandt's report. However this plays out, it would be good news if the 49ers were talking to Boone, because the offense needs as much consistency and rhythm as possible right now.

It's Week 3. Which means it's time for the 49ers to begin to resemble the team they think they will be in 2014.

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